Merge branch 'v1'

.Rbuildignore

@@ -3,3 +3,5 @@
 ^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.github
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/draft-pdf.yaml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: JOSS/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: JOSS/paper.pdf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RMAVIS
 Title: Assign Vegetation Survey Data to GB NVC Communities
-Version: 0.995
-Date: 2024-04-01
+Version: 0.999
+Date: 2024-04-16
 Authors@R: c(person(given = "Zeke",
                     family = "Marshall",
                     role = c("aut", "cre"),
@@ -22,27 +22,16 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+LazyDataCompression: xz
 Imports:
-  shiny,
-  rhandsontable,
-  reactable,
-  bslib,
-  shinyWidgets,
-  shinyjs,
-  shinybusy,
-  rmarkdown,
-  bookdown,
-  tidyverse,
-  plotly,
-  kableExtra,
-  checkmate,
-  janitor,
-  assignNVC,
-  vegan
+  dplyr,
+  readr,
+  stringr,
+  tidyr
 Suggests:
   testthat
 URL: https://github.com/ZekeMarshall/RMAVIS
 BugReports: https://github.com/ZekeMarshall/RMAVIS/issues
 Depends: 
-    R (>= 2.10)
+    R (>= 4.3)
 LazyData: true

JOSS/paper.Rmd

@@ -0,0 +1,180 @@
+---
+title: '`RMAVIS` v1.0: a R Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities.'
+tags:
+  - Vegetation science
+  - NVC
+  - Ecology
+  - Survey
+authors:
+  - name: Zeke Marshall
+    orcid: 0000-0001-9260-7827
+    affiliation: 1
+  - name: Simon Smart
+    orcid: 0000-0003-2750-7832
+    affiliation: 1
+  - name: Colin Harrower
+    orcid: 0000-0001-5070-5293
+    affiliation: 2
+affiliations:
+  - name: UK Centre for Ecology \& Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, United Kingdom
+    index: 1
+  - name: UK Centre for Ecology \& Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, United Kingdom
+    index: 2
+date: "`r Sys.Date()`"
+bibliography: paper.bib
+output:
+  html_document:
+    keep_md: yes
+---
+
+# Summary
+
+`RMAVIS` is a R Shiny application for the assignment of vegetation sample
+plot data to British National Vegetation Classification (NVC) 
+communities [@rodwell1991;@rodwell1992;@rodwell1992a;@rodwell1995;@rodwell2000].
+
+The assignment of vegetation sample plot data to established vegetation 
+classification units using computational methods is a well established and 
+recognised practice [@maciejewski2020]. 
+The results of this assignment process are used in various ways, 
+including assisting in the phase 2 habitat survey
+(or NVC survey) [@rodwell2006national] process; 
+establishing an ecological baseline and identifying important ecological 
+features such as protected habitats [@cieem2022]; 
+and in ecological restoration by providing a proxy for historical reference 
+ecosystems to target and against which to measure restoration progress 
+[@pywell2002; @gann2019; @sturbois2023].
+
+In the Great Britain (GB) the development of computational methods and programs 
+for the assignment of vegetation survey data to NVC communities began with the 
+development of TABLEFIT [@hill1989; @marrs2019] and was followed by MATCH 
+[@malloch1998].
+The most recent program, the Modular Analysis of Vegetation Information System 
+(MAVIS), was developed as a windows application in 2000 and was a DEFRA-funded
+output of the ECOFACT project [@bunce1999], with the latest version released in 
+2016 [@smart2016mavis].
+
+
+# Statement of need
+
+The requirement for a new program in the form of a R Shiny [@chang2024] 
+application arises from several needs, namely to: 
+1) accommodate updates to the NVC;
+2) provide a means to easily reproduce and attribute the results of the NVC
+assignment process;
+3) broaden and simplify access through the provision of a web-based Graphical 
+User Interface (GUI);
+and
+4) facilitate the continuous development of such NVC assignment software.
+We developed `RMAVIS` considering these needs, with the view to providing
+a reliable system for use by the GB ecology and conservation community, 
+analogous to the Engine for Relevés to Irish Communities Assignment (ERICA)
+tool [@perrin2018; @perrin2019a] developed for Ireland.
+
+# Application structure
+
+Inspired by the extensible structure of the species niche and distribution 
+modelling R shiny application `wallace` [@kass2023], we constructed `RMAVIS` with 
+a modular architecture, enabling both the easy maintenance of existing modules, 
+and easy development of additional modules in the future.
+
+`RMAVIS` currently contains a total of eighteen modules, with the fourteen main 
+modules summarised in the following table.
+
+|        **Module**       |                                                          **Description**                                                          |
+|:-----------------------:|:---------------------------------------------------------------------------------------------------------------------------------:|
+|         Sidebar         |                                Acts as the control module, containing the options for each module.                                |
+|        Data Input       |                      Facilitates the entry of data, three methods are provided: manual, upload, and example.                      |
+|     Data Validation     |                 Checks the format of the inputted data and provides means to adjust incorrectly formatted entries.                |
+|      Data Structure     | Checks the structure of the inputted data, displaying the availability of data by species and number of plots per year and group. |
+|      NVC Assignment     |                                        Displays the results of the NVC assignment process.                                        |
+|  Habitat Correspondence |           Displays the habitats from alternative habitat classifications associated with the top-fitted NVC communities.          |
+|     Floristic Tables    |             Allows the comparison of floristic tables composed from the inputted data with the NVC's floristic tables.            |
+|        Frequency        |                         Summarises the frequency of occurrence of each species across all plots over time.                        |
+|           EIVs          |         Displays the mean Hill-Ellenberg ecological indicator values (EIVs) for each plot, group of plots, and all plots.         |
+|        Diversity        |                              Displays a number of diversity metrics for each plot and group of plots.                             |
+|       MVA National      |                Constructs an ordination space using all NVC pseudo-quadrats, with sample plots added in passively.                |
+|  MVA Local, restricted  |     Constructs an ordination space using the top-fitted NVC communities pseudo-quadrats, with sample plots added in passively.    |
+| MVA Local, unrestricted |               Constructs an ordination space using the top-fitted NVC communities pseudo-quadrats and sample plots.               |
+|          Report         |                Provides the user with a downloadable report, containing user-selected outputs from the app session.               |
+
+
+
+```{r screenshot, echo=FALSE, fig.cap="The MVA module of `RMAVIS`, showing the trajectory of all sample plots from the Leith Hill Wood example dataset in the ordination spaces over time."}
+knitr::include_graphics("joss_screenshot.png") 
+``` 
+
+# Data sources
+
+`RMAVIS` depends on a number of individual datasets.
+The list of accepted species was constructed using 
+the vascular plant (*Tracheophyta*) taxa present in the 
+Botanical Society of Britain and Ireland's (BSBI) database 
+[@bsbi2024TaxonLists];
+filtered to include taxa at the genus, species, hybrid species, and subspecies 
+ranks which have an associated UK Species Inventory (UKSI) Taxon Version Key 
+(TVK); the moss (*Bryophyta*), liverwort (*Marchantiophyta*), 
+and hornwort (*Anthocerotophyta*) taxa present in the UKSI, 
+retrieved from the National Biodiversity Network (NBN), filtered to include taxa 
+at the species, species aggregate, subspecies, species sensu lato, 
+and genus ranks; and the limited number of lichen (*Lecanoromycetes*) and 
+charophyte (*Charophyta*) taxa, along with one unspecified 'algae' taxon present 
+in the NVC floristic tables.
+The NVC communities present in `RMAVIS` are composed from @rodwell1991, 
+@rodwell1992, @rodwell1992a, @rodwell1995, @rodwell2000, 
+@wallace2017, @prosser2023, and @wallace2023.
+Data for habitat correspondences is derived from: 
+the Joint Nature Conservation Committee (JNCC) Spreadsheet of Habitat 
+Correspondences [@jncc2008],
+UKHab V1.1 [@butcher2020], and
+the National Plant Monitoring Scheme (NPMS) habitat correspondences
+[@pescott2019].
+Data for the vascular plant Hill-Ellenberg values were retrieved from the
+BSBI checklists, specifically the Nitrogen Score (N)
+[@bsbi2017ellenbergN], Moisture Score (F) [@bsbi2017ellenbergF],
+Reaction Score (R) [@bsbi2017ellenbergR], Salinity Score (S)
+[@bsbi2017ellenbergS], and Light Score (L) [@bsbi2017ellenbergL] checklists. 
+The corresponding data for bryophytes was taken from BRYOATT [@hill2007].
+Four example datasets are bundled with `RMAVIS`: 
+1) Parsonage Down [@ridding2020],
+2) Leith Hill Place Wood [@wood2015; @smart2024],
+3) Whitwell Common [@smart2000],
+and
+4) Newborough Warren [@wallace2018].
+
+# Conclusion
+
+`RMAVIS` provides a web-based, easily accessible GUI for the assignment of
+vegetation sample plot data to GB NVC communities. 
+`RMAVIS` also provides a number of other exploratory analyses, 
+which compliment the NVC assignment results.
+We plan to maintain, optimise, and expand the functionality found in v1.0 of 
+`RMAVIS` and hope that it acts as a useful tool for the GB ecology and 
+conservation community.
+
+# Acknowledgements
+
+The development of `RMAVIS` was partly supported by the UK‐SCAPE program 
+delivering National Capability (NE/R016429/1) funded by the Natural Environment 
+Research Council.
+
+We would like to thank
+Lindsay Maskell,
+Lucy Ridding,
+Barry Jobson,
+Colin Conroy,
+Rob Marrs,
+Andy McMullen,
+John Handley,
+Michael Tso,
+Simon Rolph,
+Cristina Martin Hernandez,
+and
+George Linney
+for testing `RMAVIS`.
+
+We would also like to thank Laurence Jones for providing the Newborough
+Warren example dataset and Lucy Ridding for providing the Parsonage Down
+example dataset.
+
+# References